Keio Plaza is a nice standard hotel.
Great location close to Shinjuku station and a easy stop for the limo bus from the airport and for all the tours.
They have a couple of nice restaurants in case you don't feel like eating out and even a little supermarket in the basement in case the kids want a few snacks at an ungodly hour.
It ain't no Four Seasons or Park Hyatt but you can get 2 rooms for less than USD$ 500. You can also get a room with 3 beds but not sure if it would fit or if they would allow another bed.
You could always have 3 beds and one kid sleep on the floor.

When in Tokyo, I am not sure how much time you would spend in the room; Tokyo is huge, fun with tons of variety and excitement; it is also very safe at all hours of the day/night so spending lots of time outside is fun - even in the dead of winter.